How a quarter of the cow genome came from snakes

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Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome is made up of bits of DNA that have copied themselves and jumped around, creating vast tracts of repetitive sequences. The same is true for the cow genome, where one particular piece of DNA, known as BovB, has run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made of BovB sequences or their descendants.


BovB isn’t restricted to cows. If you look for it in other animals, as Ali Morton Walsh from the University of Adelaide did, you’ll find it in elephants, horses, and platypuses. It lurks among the DNA of skinks and geckos, pythons and seasnakes. It’s there in purple sea urchin, the silkworm and the zebrafish.

The obvious interpretation is that BovB was present in the ancestor of all of these animals, and stayed in their genomes as they diversified. If that’s the case, then closely related species should have more similar versions of BovB. The cow version should be very similar to that in sheep, slightly less similar to those in elephants and platypuses, and much less similar to those in snakes and lizards.

But not so. If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel universe where cows are more closely related to snakes than to elephants, and where one gecko is more closely related to horses than to other lizards.

This is because BovB isn’t neatly passed down from parent to offspring, as most pieces of animal DNA are. This jumping gene not only hops around genomes, but between them.

Written By: Ed Yong
continue to source article at phenomena.nationalgeographic.com

13 COMMENTS

  1. @antipodesman: This is nothing to do with Lamarck – he said that characteristics acquired during your lifetime somehow get passed to your children. This argument is shows evidence that genes can get “horizontally” transfered by agents such as viruses or other pathogens. Epigenetics is close to Lamarckism, but is not the same.

  2. More specifically: That somehow the phenotype ‘updates’ the genes and is so inherited. For example, a cook hands become hardened and calloused and the cook is able to pick up really hot things. Lamarckism says that the cook’s gene’s become modified so the cook’s children are born with heat-resistant hands.

    Horizontal gene transfer is where an already inheritable gene is spliced out of one organism into another.

    I hope that is clearer.

    In reply to #2 by Modeler:

    @antipodesman: This is nothing to do with Lamarck – he said that characteristics acquired during your lifetime somehow get passed to your children. This argument is shows evidence that genes can get “horizontally” transfered by agents such as viruses or other pathogens. Epigenetics is close to Lamarckism, but is not the same.

  3. OK , I have read the greatest show on earth and I have read the assertions that comparing the genetic code can lead us to knowledge on how closely related species are. I’d like to see more evidence on this , because the greatest show on earth issued this as a fact and told us nothing on why we should believe this. What about the correlation and causation argument that is constantly rolled out by rationalist. Just because something looks kind of the same it does not allow you to draw definitive conclusions. Why can’t this theory be used to order evolving bacteria samples , if it is indeed sound. Can someone please give me evidence or point me to a resource that says more than ‘they look the same!’

  4. Milk just got grosser.

    I want something better than Horizontal Gene Transfer to explain this.

    If genes are redundant, can they just be edited out and still get the same organism? That doesn’t sound right. Watching the progression of our understanding of introns, I’m comfortable saying we have no idea how genetics works, beyond making the occasional green monkey.

  5. Modeler
    You are certainly correct. Lamark was thinking of the accumulation of favourable characters through environmental effects. There is however still the effect of the transmission of “characters” to the next generation that are acquired after birth.
    I believe Darwin paid homage in the Origin to Lamark by suggesting that natural selection was only a secondary factor (though perhaps in feigned humility).

  6. Of the specific quote in Origin, is it the one Wikipedia quotes?

    He praised Lamarck for “the eminent service of arousing attention to the probability of all change in the organic… world, being the result of law, not miraculous interposition” ["Historical sketch". On the Origin of Species (3rd–6th ed.). London: John Murray]

    If so, that’s not really relevant.

    Darwin knew very little about how characteristics might be encoded or stored in living things (only that, empirically, they were). Further, he knew very little was known about how the parents’ characteristics ‘blended’ during sexual reproduction and then caused that characteristic in the offspring. As a corollary, nothing was known about how the characteristic might be introduced or modified, and so his thoughts on the matter were certainly wrong by our current understanding, and did include some ideas that were close to it. You can read more about Darwin’s thoughts re: Lamarckism here.

    I think you are confusing the origination of a new characteristic with the mechanism by which it becomes prevalent in a population. Natural selection is not about how a new characteristic occurs (known mechanisms include mutation and horizontal gene transfer), but about how it becomes dominant in a population which includes variation. In evolution, both these processes are necessary but distinct.

    [As an aside, Natural Selection itself is only one mechanism by which a characteristic can become prevalent, because random genetic drift and chance play crucial roles as well]

    In reply to #8 by antipodesman:

    Modeler
    You are certainly correct. Lamark was thinking of the accumulation of favourable characters through environmental effects. There is however still the effect of the transmission of “characters” to the next generation that are acquired after birth.
    I believe Darwin paid homage in the Origin to Lamark by suggesting that natural selection was only a secondary factor (though perhaps in feigned humility).

  7. In reply to #7 by This Is Not A Meme:

    Milk just got grosser.
    If genes are redundant, can they just be edited out and still get the same organism? That doesn’t sound right. Watching the progression of our understanding of introns, I’m comfortable saying we have no idea how genetics works, beyond making the occasional green monkey.

    Sometimes removing a single copy of a gene when there are multiples does not seem to cause an observable difference; other times having more than one copy of a gene produces more transcription of the gene, or allows the different copies of the gene to be controlled (via different promoter and demoters) by different systems.

    As an aside, the moment you have a gene duplication, you have the opportunity for the two copies to evolve different effects on the phenotype, turning a simple, broad mechanism into perhaps two more finely focused ones. Further duplication down the ages leads to whole families of similar genes producing similar but different proteins – see Larry Moran for a discussion. Granted these are not introns, though.

    I am not sure that the study of introns can lead to the conclusion that we have no idea how genetics works. I am sure that the discovery of introns and the associated mechanisms of duplication and suppression and deletion of them have greatly increased our understanding about the complexity of genetics – the study of which has lead among other things to a number of important discoveries about the nature of viruses. It also supports Richard Dawkin’s view that the the key insight to understanding life is viewing the gene as a selfish replicating unit.

  8. Hi Pauly

    There is a huge amount written on comparing genetic code that provides incredibly strong evidence for evolution. In fact, the very fact that all life on earth uses the same DNA chemistry and the same genetic code (i.e. nucleotide triplet -> amino acid) is extremely strong evidence of common ancestry. That is a bottom up argument.

    In a top down argument, there is a fantastic look at the history of chromosome 2 in humans and the correlates in chimps and gorillas that’s worth looking at: http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/

    A few of other examples of genes being used to study evolution, ranging from tracing the origin of races within the human species to deeply conserved genes across the animal kingdom.

    There’s a heck of a lot more out there, so this is simply scratching the surface.

    In reply to #6 by Pauly_:

    OK , I have read the greatest show on earth and I have read the assertions that comparing the genetic code can lead us to knowledge on how closely related species are. I’d like to see more evidence on this , because the greatest show on earth issued this as a fact and told us nothing on why we should believe this. What about the correlation and causation argument that is constantly rolled out by rationalist. Just because something looks kind of the same it does not allow you to draw definitive conclusions. Why can’t this theory be used to order evolving bacteria samples , if it is indeed sound. Can someone please give me evidence or point me to a resource that says more than ‘they look the same!’

  9. Let’s stop getting side-tracked: this fascinating study has not the smallest connection with Lamarckian inheritance of acquired characteristics, nor with “epigenetics”.

    Horizontal gene transfer is a very interesting phenomenon, which could, if it is widespread, complicate the use of molecular genetics when working out taxonomic relationships. Ideally, molecular taxonomy relies on the assumption that genes pass only vertically down the generations, in strictly diverging pedigrees. Horizontal gene transfer violates this, which is why molecular taxonomy is problematic in bacteria. Startling conclusions of molecular taxonomy, for example the close relationship of hippos and whales, could be called in question if it turned out that there was massive horizontal gene transfer.

    The BovB story is a triumphant vindication of the “selfish gene” view of life, illustrating, as it does, yet another way in which genes get themselves duplicated, breaking free of the “vehicle” (see The Extended Phenotype or, more briefly, the Second Edition of The Selfish Gene). Not content with making snakes and making cows, genes have found a way (perhaps ticks) to hop from one to the other, and they then massively self-duplicate when they get there.

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